The Last Smiley minigame has several unused levels: level3_v1.w3d, level3_v2.w3d, and level3_v3.w3d. The first unused level is an earlier version of the final game's sixth level. The second is a revised version of the first, while the third is a completely unique, unused level.

At an unknown point within the first nine months of the game's history, a Neopet was introduced that was a stylized caricature of R&B singer Macy Gray. On July 26, 2000, due to unspecified legal reasons, the Macy Gray was replaced with a different singing Neopet called the Kau.

To commemorate the Chinese New Year in early 2006, Neopets collaborated with Pepsi to include product placement in the game worldwide and host a sweepstakes exclusively in China. As it was the Year of the Dog, the prize was a limited edition royal-blue Gelert plush doll with a tag of the Pepsi logo on its collar; only 500 were known to have been made. Little has been documented about the extent of this promotional campaign, but it is known that four Flash minigames were playable outside of China in an area called Pepsi World (or Pepsi Palace) on the Neopets website before March 1, 2006: Pepsi World, Pepsi Surf Football, Pepsi Rescue, and Pepsi: Fast Flight. While none of the games are playable on the website today, the .swf Flash file for Pepsi Surf Football appears to still be stored within the website's data, along with many images used during the campaign.

When the Grey Faerie's Neopedia article was released, a "Bottled Grey Faerie" item was found in the game's servers. Neopian Times Editorial #90 would later imply that a plotline involving the Grey Faeries was on the way, however nothing has been heard about this since, likely meaning that whatever plotline was planned was either cancelled or delayed indefinitely.

On July 17, 2023, Neopets was purchased from NetDragon through a management buyout deal by Dominic Law, the Neopets Chief Metaverse Officer and former Director of New Markets at both NetDragon and Cherrypicks. This led to the formation of "World of Neopia, Inc.", a company comprised of team members from both Neopets and Neopets Metaverse, with Law serving as CEO. As part of this, it was announced that Neopets had received $4 million in investment money in early 2023, with additional funding from the management buyout equipping World of Neopia, Inc. to make "meaningful changes in pursuit of a Neopian renaissance." These changes include revamping the homepage and creating the 2024 mobile game "World of Neopets".

In September 2021, Neopets attempted to enter the budding Non-fungible Token market with a project called the "Neopets Metaverse", predictably sparking major backlash from the Neopets fandom citing pre-existing criticisms and negative stigmas surrounding NFTs. However, much less predictable were the string of controversies that followed, which involved using the fansite Dress to Impress to make their NFTs (notably signified by one of the tokens having a glitch only present on Dress to Impress and not the official Neopets site), promotion of an R-rated NFT collection titled "Horny Hedgehogs", banning the word "gay" from their Discord server but permitting homophobic slurs, portraying those opposed to NFTs as the "Soyjak" meme, and in secret planning to get the main game developers to implement long-requested features so fans would "shut up" about the NFT project.

When the project first spread, the Neopets Twitter account stated in a direct message that it was a scam, putting doubt on its legitimacy, but the main brand would later would endorse the project. The most infamous endorsement came when the winner of an art contest ended up being an anti-NFT protest image, which they removed and - after being called out - subtly censored it by compressing it so hard that it couldn't be read without extremely close observance.

After two years, Neopets ultimately announced in July 2023 that it would be completely shuttering the Neopets Metaverse project after former CEO of the Metaverse division Dominic Law brokered a "management buyout deal", and that the game would no longer have any cryptocurrency or NFT elements.

To promote the release of Petpet Park, Neopets began a new mini plot in September 2008 to help set up the game's events. Users were made agents of the Petpet Protection League and tasked with helping the Petpets cross over from their original home of Petaria into the titular Petpet Park. Over the next several weeks, users solved various puzzles and helped the six primary Petpet species reach Petpet Park, learning info about the individual species in the process (i.e. temperment, favorite foods, and special skills) as well as Petpet Park's storyline. On October 27, the Mission Headquarters was updated, and users who successfully helped the Petpets recieved rewrds such as Neopoints, a site theme, and a Petpet Park-themed wearable.

Neopets' former CEO Dough Dohring was an avid Scientologist, and used L. Ron Hubbard's "Org Board" method for running the business. Neopets founders Adam and Donna Powell were unaware of Dohring's ties to the cult when signing on to allow him to run the company, and it supposedly did not affect the inner workings of the company, though most of the employees were Scientologists and Dohring would often propose implementing Scientology education into the website. Williams would claim of the ownership in a 2014 Reddit AMA:


Dohring would leave Neopets after it was acquired by Viacom in 2005.

To promote the release of Sonic and the Black Knight, Neopets released a browser game called "Sonic Knight in Training", where Sonic must use Caliburn to deflect apples shot at him from the three Knights of the Round Table (Lancelot, Gawain, and Percival). If the player received a high enough score, they would unlock a then-new trailer for the game.

In the files of the Neopets promotional game Pepsi Surf Football, you can find a shortened audio clip from a trailer for the film Lilo & Stitch, featuring a narrator saying "His name is Stitch" with "Back in Black" by AC/DC playing in the background.

In the files for the Neopets promotional game Alvin and the Chipmunks: How Many Chipmunks Could You Fit in Your Room Without Your Mom Finding Out?, you can find leftovers from the previous promotional game The Chronicles of Narnia: Prince Caspian Personality Quiz.

The original version of the Bruce Neopet was a photograph of the British celebrity Bruce Forsyth. This was changed to an illustration of Forsyth, and eventually an anthropomorphic penguin.